rs10510905

Variant names:

• chr3-63811196-T-C
• rs10510905
• XM_047447470.1:c.-79-12054T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443346.1(ENSG00000293415):​n.622+15628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 152,250 control chromosomes in the GnomAD database, including 1,226 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.083 (1226 hom., cov: 32)
• Consequence: ENSG00000293415 ENST00000443346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 1 publications found

Genes affected

C3orf49 (HGNC:25190): (chromosome 3 open reading frame 49)

ENSG00000293415 (HGNC:):

CDHR18P (HGNC:53742): (cadherin related family member 18, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443346.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDHR18P	NR_197413.1		n.110+2332A>G		intron	N/A
	CDHR18P	NR_197414.1		n.110+2332A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293415	ENST00000443346.1	TSL:3	n.622+15628A>G		intron	N/A
	ENSG00000293415	ENST00000792822.1		n.110+2332A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12633 AN: 152132 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0828

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0833 AC: 12677 AN: 152250 Hom.: 1226 Cov.: 32 AF XY: 0.0802 AC XY: 5971 AN XY: 74438

African (AFR) AF: 0.232 AC: 9632 AN: 41520

American (AMR) AF: 0.0527 AC: 806 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0325 AC: 113 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5182

South Asian (SAS) AF: 0.0331 AC: 160 AN: 4834

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0218 AC: 1482 AN: 68030

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0541 Hom.: 168

Bravo AF: 0.0907

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10510905;

hg19: chr3-63796872;